Substitute Jake Speight scored with his first touch to extend Wrexham's unbeaten to 13 games and reclaim top spot in the Blue Square Bet Premier.
Marc Bridge-Wilkinson put the visitors ahead on 35 minutes from the penalty spot after Mark Creighton's wild lunge.
Sam Russell denied Adrian Cieslewicz with a superb save, but Ryan Bowman missed a sitter to double the lead.
Cieslewicz equalised after a goalmouth scramble before Speight hit the winner from a planned free-kick on 81 minutes.
With the Darlington defence expecting a cross, Johnny Hunt played the ball low and square towards the penalty spot, and Speight drilled the ball past Russell after losing his marker.
The striker should have put the game beyond the visitors in stoppage time after a smart turn, but he fired straight at Russell.
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Wrexham manager Andy Morrell told BBC Radio Wales: "Not pretty, I have to say. But the result is all that matters in the end isn't it.
"We've come out victors, whether we deserved it or not I'm not too sure, but hey let's take them and run.
"Three points and back to the top."